Ian, thanks for the release! How hard would it be to change the main color to yellow?

Not too hard, but maybe a little time consuming.. You have PS, open each icon and wallpaper and use the same Hue & Saturation on each, try the hue to about -142 with the wallpaper, red looks pretty good too.

Really need a screenshot to see what's happening. Check you have "SummerBoard" switched on in Winterboard.
If you have "Shrink" installed... uninstall it.
Screenshot will help us see if you have the 5 rows set-up okay.